[gmx-users] g_hbond tool question

Carlos Navarro Retamal cnavarro at utalca.cl
Wed Nov 19 04:01:08 CET 2014

Dear gromacs users,  
I’m studying the hydrogen bond interaction between a protein and different solvents.To do that i’m using the g_hbond tools of gromacs (4.6.3 version).
As groups,I started using ‘Protein’ and ‘Sol’ and i got an specific number.
After that, to analyse the interaction in a more specific way between this 2 groups, i ran the g_hbond tools using different groups:
'MainChain+Cb' - 'SOL'
'MainChain+H'   - ‘SOL'
'SideChain'        -  'SOL'
'SideChain+H’   -  ‘SOL’
But when i sum hbond got by these four selections i got different values (higher) than the values got from ‘Protein’ - ‘SOL’
Why is this happening? Am i interpreting in a wrong way what the selection ‘Protein’ - ‘SOL’ is considering?
Hope someone can help me.
Thanks in advances,

Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

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